In this project, we have 38 individuals and collected
PBMC in two timepoints: before BCG vaccination and 3 months
BCG vaccination. In each timepoint, the PBMCs were stimulated
with/without LPS. In total, we have four conditions, Baseline
BCG effect, LPS effect and BCG+LPS effect.
Analysis
We performed three analysis using different models.
limix_qtl[1] was used in this project. For the Main Effect,
we combined four conditions together per cell type and
calculated the SNP and eGene correlation. For the Interaction Effect
we add G*E as the interaction term. For the Trained Immunity Effect
we focus on monocytes and calculated the correlation between SNP
and gene expression changes between two conditions (BCG+LPS and LPS).
Details of eQTL
Cell-type eQTL (Left): The main effect in each cell type.
In this mode, four conditions are
combined to identified the main effect in each cell type.
Response eQTL (Middel): BCG effect, LPS
effect and LPS effect under BCG condition
are calculated in each cell type.
Trained Immunity eQTL (Right): Trained immunity effect
is calcualted in monocytes. The gene expression difference is used as
phenotype.